The infant gut virome is associated with preschool asthma risk independently of bacteria

Bacteriophage (also known as phage) communities that inhabit the gut have a major effect on the structure and functioning of bacterial populations, but their roles and association with health and disease in early life remain unknown. Here, we analyze the gut virome of 647 children aged 1 year from the Copenhagen Prospective Studies on Asthma in Childhood2010 (COPSAC2010) mother-child cohort, all deeply phenotyped from birth and with longitudinally assessed asthma diagnoses. Specific temperate gut phage taxa were found to be associated with later development of asthma. In particular, the joint abundances of 19 caudoviral families were found to significantly contribute to this association. Combining the asthma-associated virome and bacteriome signatures had additive effects on asthma risk, implying an independent virome-asthma association. Moreover, the virome-associated asthma risk was modulated by the host TLR9 rs187084 gene variant, suggesting a direct interaction between phages and the host immune system. Further studies will elucidate whether phages, alongside bacteria and host genetics, can be used as preclinical biomarkers for asthma.

Drug dosage modifications in 24 million in-patient prescriptions covering eight years: A Danish population-wide study of polypharmacy

Polypharmacy has generally been assessed by raw counts of different drugs administered concomitantly to the same patients; not with respect to the likelihood of dosage-adjustments. To address this aspect of polypharmacy, the objective of the present study was to identify co-medications associated with more frequent dosage adjustments. The data foundation was electronic health records from 3.2 million inpatient admissions at Danish hospitals (2008-2016). The likelihood of dosage-adjustments when two drugs were administered concomitantly were computed using Bayesian logistic regressions. We identified 3,993 co-medication pairs that associate significantly with dosage changes when administered together. Of these pairs, 2,412 (60%) did associate with readmission, mortality or longer stays, while 308 (8%) associated with reduced kidney function. In comparison to co-medications pairs that were previously classified as drug-drug interactions, pairs not classified as drug-drug interactions had higher odds ratios of dosage modifications than drug pairs with an established interaction. Drug pairs not corresponding to known drug-drug interactions while still being associated significantly with dosage changes were prescribed to fewer patients and mentioned more rarely together in the literature. We hypothesize that some of these pairs could be associated with yet to be discovered interactions as they may be harder to identify in smaller-scale studies.

Expanding known viral diversity in the healthy infant gut

The gut microbiome is shaped through infancy and impacts the maturation of the immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis and lysogeny, with the latter being especially prominent in the infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes and standardized detection methods. Here we systematically resolved the viral diversity in faecal viromes from 647 1-year-olds belonging to Copenhagen Prospective Studies on Asthma in Childhood 2010, an unselected Danish cohort of healthy mother-child pairs. By assembly and curation we uncovered 10,000 viral species from 248 virus family-level clades (VFCs). Most (232 VFCs) were previously unknown, belonging to the Caudoviricetes viral class. Hosts were determined for 79% of phage using clustered regularly interspaced short palindromic repeat spacers within bacterial metagenomes from the same children. Typical Bacteroides-infecting crAssphages were outnumbered by undescribed phage families infecting Clostridiales and Bifidobacterium. Phage lifestyles were conserved at the viral family level, with 33 virulent and 118 temperate phage families. Virulent phages were more abundant, while temperate ones were more prevalent and diverse. Together, the viral families found in this study expand existing phage taxonomy and provide a resource aiding future infant gut virome research.

Language-agnostic pharmacovigilant text mining to elicit side effects from clinical notes and hospital medication records

We sought to craft a drug safety signalling pipeline associating latent information in clinical free text with exposures to single drugs and drug pairs. Data arose from 12 secondary and tertiary public hospitals in two Danish regions, comprising approximately half the Danish population. Notes were operationalised with a fastText embedding, based on which we trained 10,720 neural-network models (one for each distinct single-drug/drug-pair exposure) predicting the risk of exposure given an embedding vector. We included 2,905,251 admissions between May 2008 and June 2016, with 13,740,564 distinct drug prescriptions; the median number of prescriptions was 5 (IQR: 3-9) and in 1,184,340 (41%) admissions patients used ≥5 drugs concomitantly. 10,788,259 clinical notes were included, with 179,441,739 tokens retained after pruning. Of 345 single-drug signals reviewed, 28 (8.1%) represented possibly undescribed relationships; 186 (54%) signals were clinically meaningful. 16 (14%) of the 115 drug-pair signals were possible interactions and 2 (1.7%) were known. In conclusion, we built a language-agnostic pipeline for mining associations between free-text information and medication exposure without manual curation, predicting not the likely outcome of a range of exposures, but the likely exposures for outcomes of interest. Our approach may help overcome limitations of text mining methods relying on curated data in English and can help leverage non-English free text for pharmacovigilance.

Drug interactions in hospital prescriptions in Denmark: Prevalence and associations with adverse outcomes

Purpose

While the beneficial effects of medications are numerous, drug–drug interactions may lead to adverse drug reactions that are preventable causes of morbidity and mortality. Our goal was to quantify the prevalence of potential drug–drug interactions in drug prescriptions at Danish hospitals, estimate the risk of adverse outcomes associated with discouraged drug combinations, and highlight the patient types (defined by the primary diagnosis of the admission) that appear to be more affected.

Methods

This cross‐sectional (descriptive part) and cohort study (adverse outcomes part) used hospital electronic health records from two Danish regions (~2.5 million people) from January 2008 through June 2016. We included all inpatients receiving two or more medications during their admission and considered concomitant prescriptions of potentially interacting drugs as per the Danish Drug Interaction Database. We measured the prevalence of potential drug–drug interactions in general and discouraged drug pairs in particular during admissions and associations with adverse outcomes: post‐discharge all‐cause mortality rate, readmission rate and length‐of‐stay.

Results

Among 2 886 227 hospital admissions (945 475 patients; median age 62 years [IQR: 41–74]; 54% female; median number of drugs 7 [IQR: 4–11]), patients in 1 836 170 admissions were exposed to at least one potential drug–drug interaction (659 525 patients; median age 65 years [IQR: 49–77]; 54% female; median number of drugs 9 [IQR: 6–13]) and in 27 605 admissions to a discouraged drug pair (18 192 patients; median age 68 years [IQR: 58–77]; female 46%; median number of drugs 16 [IQR: 11–22]). Meropenem‐valproic acid (HR: 1.5, 95% CI: 1.1–1.9), domperidone‐fluconazole (HR: 2.5, 95% CI: 2.1–3.1), imipramine‐terbinafine (HR: 3.8, 95% CI: 1.2–12), agomelatine‐ciprofloxacin (HR: 2.6, 95% CI: 1.3–5.5), clarithromycin‐quetiapine (HR: 1.7, 95% CI: 1.1–2.7) and piroxicam‐warfarin (HR: 3.4, 95% CI: 1–11.4) were associated with elevated mortality. Confidence interval bounds of pairs associated with readmission were close to 1; length‐of‐stay results were inconclusive.

Conclusions

Well‐described potential drug–drug interactions are still missed and alerts at point of prescription may reduce the risk of harming patients; prescribing clinicians should be alert when using strong inhibitor/inducer drugs (i.e. clarithromycin, valproic acid, terbinafine) and prevalent anticoagulants (i.e. warfarin and non‐steroidal anti‐inflammatory drugs ‐ NSAIDs) due to their great potential for dangerous interactions. The most prominent CYP isoenzyme involved in mortality and readmission rates was 3A4.

Using Machine Learning to Identify Patients at High Risk of Inappropriate Drug Dosing in Periods with Renal Dysfunction

Purpose

Dosing of renally cleared drugs in patients with kidney failure often deviates from clinical guidelines, so we sought to elicit predictors of receiving inappropriate doses of renal risk drugs.

Patients and methods

We combined data from the Danish National Patient Register and in-hospital data on drug administrations and estimated glomerular filtration rates for admissions between 1 October 2009 and 1 June 2016, from a pool of about 2.6 million persons. We trained artificial neural network and linear logistic ridge regression models to predict the risk of five outcomes (>0, ≥1, ≥2, ≥3 and ≥5 inappropriate doses daily) with index set 24 hours after admission. We used time-series validation for evaluating discrimination, calibration, clinical utility and explanations.

Results

Of 52,451 admissions included, 42,250 (81%) were used for model development. The median age was 77 years; 50% of admissions were of women. ≥5 drugs were used between admission start and index in 23,124 admissions (44%); the most common drug classes were analgesics, systemic antibacterials, diuretics, antithrombotics, and antacids. The neural network models had better discriminative power (all AUROCs between 0.77 and 0.81) and were better calibrated than their linear counterparts. The main prediction drivers were use of anti-inflammatory, antidiabetic and anti-Parkinson's drugs as well as having a diagnosis of chronic kidney failure. Sex and age affected predictions but slightly.

Conclusion

Our models can flag patients at high risk of receiving at least one inappropriate dose daily in a controlled in-silico setting. A prospective clinical study may confirm that this holds in real-life settings and translates into benefits in hard endpoints.

Linking glycemic dysregulation in diabetes to symptoms, comorbidities, and genetics through EHR data mining

Diabetes is a diverse and complex disease, with considerable variation in phenotypic manifestation and severity. This variation hampers the study of etiological differences and reduces the statistical power of analyses of associations to genetics, treatment outcomes, and complications. We address these issues through deep, fine-grained phenotypic stratification of a diabetes cohort. Text mining the electronic health records of 14,017 patients, we matched two controlled vocabularies (ICD-10 and a custom vocabulary developed at the clinical center Steno Diabetes Center Copenhagen) to clinical narratives spanning a 19 year period. The two matched vocabularies comprise over 20,000 medical terms describing symptoms, other diagnoses, and lifestyle factors. The cohort is genetically homogeneous (Caucasian diabetes patients from Denmark) so the resulting stratification is not driven by ethnic differences, but rather by inherently dissimilar progression patterns and lifestyle related risk factors. Using unsupervised Markov clustering, we defined 71 clusters of at least 50 individuals within the diabetes spectrum. The clusters display both distinct and shared longitudinal glycemic dysregulation patterns, temporal co-occurrences of comorbidities, and associations to single nucleotide polymorphisms in or near genes relevant for diabetes comorbidities.

Somatostatin inhibition of secretagogue and forskolin-stimulated gastric acid secretion

The action of somatostatin (SS) on acid secretion and histamine release was studied in isolated gastric mucosa of toads mounted in Ussing chambers. SS inhibited H+ secretion and histamine release stimulated by cholinergic and gastrinergic secretagogues. Exogenous histamine stimulation of H+ secretion was blocked noncompetitively by SS in a dose-dependent manner. In mucosae maximally stimulated by histamine or forskolin and cimetidine, acetylcholine (ACh) and tetragastrin (TG) induced a direct stimulation of the oxyntopeptic cell not inhibited by SS. Indomethacin, an inhibitor of prostaglandin synthesis, did not prevent SS inhibition of histamine stimulation. Pretreatment with SS abolished forskolin stimulation of H+ secretion. SS induced a small inhibition of the stimulatory effect of N6, 2'-O-dibutyryladenosine 3',5'-cyclic monophosphate. These results suggest that SS inhibits acid secretion stimulated by secretagogues through different mechanisms: 1) inhibition of histamine release by ACh and TG, 2) inhibition of endogenous and exogenous histamine stimulation through a blockade of adenylate cyclase, and 3) an inhibitory effect subsequent to the synthesis of adenosine 3',5'-cyclic monophosphate. The direct activation of the oxyntopeptic cell by ACh and TG does not seem to be affected by somatostatin.